Contacts of the strand formed by residues 2060 - 2071 (chain 2) in PDB entry 1BMV
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PHE2060 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20332 LEU 3.4 13.5 - - - -
20342 SER* 5.1 0.4 - - - -
20352 ILE* 2.9 45.8 - - + -
20542 LEU* 4.2 4.7 - - + -
20572 TRP* 4.8 5.8 - - + -
20582 ARG 4.3 0.2 + - - -
20592 TYR* 1.3 76.1 - - - +
20612 VAL* 1.3 83.3 + - - +
20642 LEU* 4.0 12.3 - - + -
21252 ALA* 4.0 0.4 - - - -
21262 TRP* 2.7 67.7 + + - +
21282 THR* 3.9 20.4 - - - +
21692 ILE* 3.6 31.9 - - + -
21722 MET* 4.2 19.3 - - + -
21732 CYS 3.4 8.7 - - - +
21742 ALA* 5.0 0.7 - - - -
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Residues in contact with VAL2061 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20602 PHE* 1.3 80.7 - - - +
20622 GLY* 1.3 63.7 - - - +
21192 GLN* 4.6 16.6 - - + +
21222 PHE* 4.5 12.3 - - + +
21232 LEU 6.0 0.4 - - - -
21242 THR 4.8 1.1 - - - -
21252 ALA* 3.5 31.6 - - + +
21262 TRP* 3.5 28.5 - - + -
21692 ILE* 4.3 0.3 - - - +
21722 MET* 3.3 25.3 - - - +
21732 CYS* 3.0 30.3 + - + +
21752 TYR* 4.3 6.3 - - + -
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Residues in contact with GLY2062 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20612 VAL* 1.3 82.6 - - - +
20632 ASP* 1.3 66.9 + - - -
20642 LEU* 3.8 8.6 + - - +
21192 GLN* 3.7 18.8 - - - +
21222 PHE* 4.0 10.4 - - - -
21262 TRP* 4.6 0.5 - - - -
21692 ILE* 4.5 4.0 - - - -
21702 GLU 3.9 1.6 - - - -
21712 ASN 3.6 21.3 - - - -
21722 MET* 4.0 3.1 - - - -
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Residues in contact with ASP2063 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20622 GLY* 1.3 71.9 - - - -
20642 LEU* 1.3 60.9 + - - +
20652 VAL* 3.7 0.6 + - - +
21162 LYS* 4.2 19.7 + - - -
21172 PHE 3.5 14.6 - - - +
21182 SER* 4.1 4.1 + - - -
21192 GLN* 2.7 42.3 + - - +
21682 ILE 3.4 2.6 - - - +
21692 ILE* 3.2 6.4 - - - -
21702 GLU* 2.5 59.5 + - + +
21712 ASN* 3.4 10.4 - - - +
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Residues in contact with LEU2064 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20332 LEU* 3.6 28.3 - - + -
20352 ILE* 5.8 0.2 - - + -
20602 PHE* 4.0 12.3 - - + -
20622 GLY 3.9 12.3 - - - +
20632 ASP* 1.3 74.7 - - - +
20652 VAL* 1.3 61.9 + - - +
20662 PHE* 3.2 28.0 - - + -
21162 LYS* 4.0 0.3 - - - -
21172 PHE* 3.1 32.4 + - + +
21222 PHE* 4.1 9.6 - - + -
21262 TRP* 3.5 28.9 - - + -
21662 LEU* 4.1 5.8 - - + -
21682 ILE 4.1 1.6 - - - -
21692 ILE* 3.0 37.7 - - + -
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Residues in contact with VAL2065 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20632 ASP 4.9 2.0 - - - +
20642 LEU* 1.3 72.2 - - - +
20662 PHE* 1.3 66.6 + - - +
21142 VAL* 4.8 13.9 - - + -
21152 LEU 3.5 6.7 - - - +
21162 LYS* 3.4 35.7 - - + -
21662 LEU* 3.6 4.4 - - - +
21672 THR* 3.0 48.6 + - + -
21682 ILE* 3.1 33.0 + - + +
21702 GLU* 4.3 8.5 - - - +
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Residues in contact with PHE2066 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20152 MET* 3.8 17.5 - - + -
20312 MET* 6.3 0.2 - - - -
20332 LEU* 3.9 19.1 - - + -
20642 LEU* 3.2 33.9 - - + -
20652 VAL* 1.3 76.1 - - - +
20672 GLU* 1.3 59.5 + - - +
20682 VAL* 4.1 3.4 - - + -
20842 ILE* 5.7 2.2 - - + -
21142 VAL* 3.7 4.7 - - - +
21152 LEU* 2.7 52.0 + - + +
21172 PHE* 3.9 21.1 - + + -
21442 LEU* 4.6 20.6 - - + -
21642 VAL* 3.8 26.0 - - + -
21652 LYS 3.5 2.0 - - - -
21662 LEU* 2.4 42.0 - - + -
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Residues in contact with GLU2067 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20652 VAL* 6.2 0.2 - - + -
20662 PHE* 1.3 74.8 - - - +
20682 VAL* 1.3 62.1 + - - +
20692 SER* 3.8 7.9 + - - +
21122 LYS* 3.5 48.2 + - + +
21132 VAL 3.8 2.7 - - - -
21142 VAL* 4.5 14.9 - - + +
21632 GLY 3.3 6.2 - - - +
21642 VAL* 3.5 0.2 - - - -
21652 LYS* 2.9 55.8 + - + +
21672 THR* 3.8 22.0 + - + +
31132 GLU* 4.6 5.2 - - - +
2M G 5.6 1.7 - - - +
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Residues in contact with VAL2068 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20662 PHE* 4.4 2.9 - - + -
20672 GLU* 1.3 80.6 - - - +
20692 SER* 1.3 58.7 - - - +
20822 PHE* 3.5 36.1 - - + -
21042 VAL* 5.2 1.1 - - + -
21062 PHE* 3.8 18.0 - - + -
21112 GLU 3.7 0.5 - - - +
21122 LYS* 3.6 3.3 - - - -
21132 VAL* 2.8 44.0 + - + +
21152 LEU* 3.4 30.5 - - + -
21622 ILE* 3.6 20.9 - - + -
21632 GLY 3.4 3.6 - - - -
21642 VAL* 4.4 11.7 - - + -
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Residues in contact with SER2069 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20142 TRP* 5.5 3.1 - - - -
20672 GLU* 4.0 9.9 + - - +
20682 VAL* 1.3 75.4 - - - +
20702 LYS* 1.3 64.6 + - - +
21062 PHE* 4.7 1.3 - - - -
21112 GLU* 3.2 13.5 - - - -
21122 LYS* 4.4 13.4 - - - +
21622 ILE* 2.9 27.5 - - - +
21632 GLY 2.9 21.6 + - - -
21652 LYS* 6.0 1.0 - - - +
31142 LEU* 4.3 29.3 - - - +
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Residues in contact with LYS2070 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20692 SER* 1.3 75.2 - - - +
20712 MET* 1.3 64.8 + - - +
20722 THR* 4.3 12.8 - - + +
20732 SER 5.0 0.2 - - - -
20742 PRO* 3.8 26.6 + - - +
20762 ILE 5.6 2.5 - - - +
20772 LYS* 6.0 0.6 - - - +
21062 PHE* 3.7 41.1 + - + +
21072 GLY 3.0 9.5 + - - -
21082 GLU* 2.9 29.1 + - - +
21102 GLN 2.9 24.9 + - - +
21112 GLU* 3.0 22.9 + - + +
21602 PHE* 5.3 8.5 - - + -
21612 VAL 3.8 3.8 - - - +
21622 ILE* 4.3 5.4 - - + -
31142 LEU* 5.3 1.7 - - - +
31162 ASN* 3.9 16.4 - - - +
31192 CYS* 3.9 11.0 - - - -
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Residues in contact with MET2071 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20142 TRP* 3.7 26.0 - - + -
20172 LYS* 5.0 3.6 - - + -
20692 SER 4.0 5.6 - - - +
20702 LYS* 1.3 82.4 - - - +
20722 THR* 1.2 64.0 + - - +
21612 VAL* 2.9 20.7 + - - +
21622 ILE 4.4 0.2 - - - -
21632 GLY* 3.9 16.2 - - - -
30852 GLY 4.4 5.4 - - - +
30872 ALA* 3.6 14.1 - - + +
31142 LEU* 2.9 39.7 - - + -
31162 ASN* 3.7 10.6 + - - +
31532 VAL* 3.7 24.5 - - + -
31542 THR* 2.9 43.2 - - + +
31572 THR* 4.7 0.5 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il